I had the same issue after installing windows on another drive. Go to the 'boot' drive, probably the drive you used to have Windows on. Make sure 'show hidden operating system files' is checked and find a file called boot.ini.
Change the timeout line to 1 and delete one of the Windows 2000 entries. Problem is which one. Easy solution: after setting timeout to 1 take note of which entry is 'default'. Boot the PC, if it's the right one delete the other.
In my case one says disk(0) the other says disk(1). The new Windows copy was on my second drive, so I deleted the disk(0) entry.